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helperFann.c
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helperFann.c
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/*
* Mex interface for the FANN library
*/
#include "helperFann.h"
#include <stdio.h>
#include "math.h"
// Note that all the code here relies on the way matlab passes arrays, this is different than in C!
//--------------------------------------------------------------------------------------------------------
/* Function code adapted from:
http://leenissen.dk/fann/forum/viewtopic.php?p=719&sid=1661ac359e28908e704231faa6310518
*/
struct fann_train_data *read_from_array(const double *din,
const double *dout,
const unsigned int num_data,
const unsigned int num_input,
const unsigned int num_output) {
unsigned int i, j;
fann_type *data_input, *data_output;
struct fann_train_data *data = (struct fann_train_data *) malloc(sizeof(struct fann_train_data));
if(data == NULL) {
fann_error(NULL, FANN_E_CANT_ALLOCATE_MEM);
return NULL;
}
fann_init_error_data((struct fann_error *) data);
data->num_data = num_data;
data->num_input = num_input;
data->num_output = num_output;
data->input = (fann_type **) calloc(num_data, sizeof(fann_type *));
if(data->input == NULL) {
fann_error(NULL, FANN_E_CANT_ALLOCATE_MEM);
fann_destroy_train(data);
return NULL;
}
data->output = (fann_type **) calloc(num_data, sizeof(fann_type *));
if(data->output == NULL) {
fann_error(NULL, FANN_E_CANT_ALLOCATE_MEM);
fann_destroy_train(data);
return NULL;
}
data_input = (fann_type *) calloc(num_input * num_data, sizeof(fann_type));
if(data_input == NULL) {
fann_error(NULL, FANN_E_CANT_ALLOCATE_MEM);
fann_destroy_train(data);
return NULL;
}
data_output = (fann_type *) calloc(num_output * num_data, sizeof(fann_type));
if(data_output == NULL) {
fann_error(NULL, FANN_E_CANT_ALLOCATE_MEM);
fann_destroy_train(data);
return NULL;
}
//Code changed to support the way matlab passes arrays
for(i = 0; i != num_data; i++) {
data->input[i] = data_input;
data_input += num_input;
for(j = 0; j != num_input; j++) {
data->input[i][j] = din[(j*num_data)+i];
//printf("input (%i,%i) = %f\n",i,j,data->input[i][j]);
}
data->output[i] = data_output;
data_output += num_output;
for(j = 0; j != num_output; j++) {
data->output[i][j] = dout[(j*num_data)+i];
//printf("output (%i,%i) = %f\n",i,j,data->output[i][j]);
}
}
return data;
}
//--------------------------------------------------------------------------------------------------------
struct fann* createNetwork( const unsigned int numLayers,
const unsigned int* layers,
const float connectionRate
){
struct fann *ann = fann_create_sparse_array(connectionRate, numLayers, layers);
fann_randomize_weights(ann, -1, 1);
fann_set_activation_function_hidden(ann, FANN_SIGMOID_SYMMETRIC);
fann_set_activation_function_output(ann, FANN_LINEAR);
fann_set_training_algorithm(ann, FANN_TRAIN_RPROP);
fann_set_train_error_function(ann, FANN_ERRORFUNC_LINEAR);
//fann_set_train_error_function(ann, FANN_ERRORFUNC_TANH);
fann_set_train_stop_function(ann, FANN_STOPFUNC_MSE);
return ann;
}
//--------------------------------------------------------------------------------------------------------
struct fann* trainNetwork(struct fann *ann,
struct fann_train_data *data,
const float desiredError,
const unsigned int maxEpochs
){
const unsigned int epochsBetweenReports = 0;
//train the network
fann_train_on_data(ann, data, maxEpochs, epochsBetweenReports, desiredError);
return ann;
}
//--------------------------------------------------------------------------------------------------------
//Evaluate the ann on an array of samples
void evaluateNetwork(struct fann *ann, const double *input, double* output, const unsigned int numData){
int i,j;
unsigned int numInputs = fann_get_num_input(ann);
unsigned int numOutputs = fann_get_num_output(ann);
fann_type *in = malloc(numInputs * sizeof(fann_type));
if(in == NULL) {
fann_error(NULL, FANN_E_CANT_ALLOCATE_MEM);
}
fann_type *out;
for(i=0;i<numData;++i){
//printf("adding to input: ");
for(j=0;j<numInputs;j++) {
in[j] = input[(j*numData)+i];
//printf("%f ",in[j]);
}
//printf("\n");
out = fann_run(ann,in);
//printf("adding to output: ");
for(j=0;j<numOutputs;j++) {
output[(j*numData)+i] = out[j];
//printf("%f ",out[j]);
}
//printf("\n");
}
free(in);
}
//--------------------------------------------------------------------------------------------------------
mxArray* createMatlabStruct(struct fann* ann, mxArray* layers, const float connectivity){
//The struct field names
const char *fnames[] = {"layers","weights","from","to", "connectivity"};
//the struct itself
mxArray* str = mxCreateStructMatrix(1, 1, 5, fnames);
//Get the connection information
unsigned int numConnections = fann_get_total_connections(ann);
struct fann_connection *connections = malloc(sizeof(struct fann_connection) * numConnections);
if(connections == NULL) {
fann_error(NULL, FANN_E_CANT_ALLOCATE_MEM);
}
fann_get_connection_array(ann, connections);
mxArray* weights = mxCreateDoubleMatrix(numConnections, 1, mxREAL);
mxArray* from = mxCreateDoubleMatrix(numConnections, 1, mxREAL);
mxArray* to = mxCreateDoubleMatrix(numConnections, 1, mxREAL);
mxArray* conn = mxCreateDoubleMatrix(1, 1, mxREAL);
double* w = mxGetPr(weights);
double* f = mxGetPr(from);
double* t = mxGetPr(to);
double* c = mxGetPr(conn);
c[0] = connectivity;
unsigned int index;
for (index = 0; index < numConnections; index++) {
w[index] = connections[index].weight;
f[index] = connections[index].from_neuron;
t[index] = connections[index].to_neuron;
//printf("Adding triple %f\t%f\t%f\n",w[index],f[index],t[index]);
}
//Free the connections memory
free(connections);
//Set all the fields on the matlab struct
mxSetFieldByNumber(str, 0, 0, layers);
mxSetFieldByNumber(str, 0, 1, weights);
mxSetFieldByNumber(str, 0, 2, from);
mxSetFieldByNumber(str, 0, 3, to);
mxSetFieldByNumber(str, 0, 4, conn);
return str;
}
//--------------------------------------------------------------------------------------------------------
float getConnectivity(const mxArray* str){
mxArray* conn = mxGetFieldByNumber(str,0, 4);
return (float)mxGetScalar(conn);
}
//--------------------------------------------------------------------------------------------------------
mxArray* getLayers(const mxArray* str){
return mxGetFieldByNumber(str,0, 0);
}
//--------------------------------------------------------------------------------------------------------
struct fann* createFannFromMatlabStruct(const mxArray* str){
//read all the fields from the matlab structure
mxArray* layers = mxGetFieldByNumber(str,0, 0);
mxArray* weights = mxGetFieldByNumber(str,0, 1);
mxArray* from = mxGetFieldByNumber(str,0, 2);
mxArray* to = mxGetFieldByNumber(str,0, 3);
mxArray* conn = mxGetFieldByNumber(str,0, 4);
unsigned int numLayers = mxGetN(layers);
double* tmpLayers = mxGetPr(layers);
double* w = mxGetPr(weights);
double* f = mxGetPr(from);
double* t = mxGetPr(to);
float c = (float)mxGetScalar(conn);
//get the layers
int j=0;
unsigned int *l = malloc(numLayers * sizeof(unsigned int));
if(l == NULL) {
fann_error(NULL, FANN_E_CANT_ALLOCATE_MEM);
}
for(j=0;j<numLayers;j++) {
l[j] = (unsigned int) tmpLayers[j];
}
//Create the network
struct fann *ann = createNetwork(numLayers,l,c);
//can I free the l array here?
//Create an array of connection structures
unsigned int numConnections = mxGetM(weights);
struct fann_connection *connections = malloc(sizeof(struct fann_connection) * numConnections);
if(connections == NULL) {
fann_error(NULL, FANN_E_CANT_ALLOCATE_MEM);
}
//fill it up
unsigned int index;
for (index = 0; index < numConnections; index++) {
connections[index].weight = w[index];
connections[index].from_neuron = f[index];
connections[index].to_neuron = t[index];
//printf("Setting triple %f\t%f\t%f\n",w[index],f[index],t[index]);
}
//Now set the connections on the network
fann_set_weight_array(ann, connections, numConnections);
//release memory for the connections array
free(connections);
return ann;
}
//--------------------------------------------------------------------------------------------------------
int main(){
return 0;
}
//--------------------------------------------------------------------------------------------------------